4. Bioenergetics Flashcards
What is ATP? (loosely)
chemical energy
What are the two sets of reactions within metabolism?
Catabolic and anabolic reactions
What does TEA stand for?
Terminal electron acceptor
What are the electron donors for eukaryotes?
Organic compounds
What is the terminal electron acceptor for eukaryotes?
O2
What are the electron donors for lithoautotrophic prokaryotes?
H2, H2S, …
What is the terminal electron acceptor for lithoautotrophic prokaryotes?
Fe(OH)3
What does litho mean?
The electron source (donors) are inorganic
What does auto mean?
Doesn’t require organic carbon, it fixes its own CO2 to assemble it into organic molecules for itself
How do microbes obtain energy? (Get ATP)
By doing a complex set of redox reactions (redox = oxidation reduction reactions)
What is anabolism?
Biochemical reactions involved in the synthesis of compounds and macromolecules such as proteins and nucleic acids
What is catabolism?
Biochemical reactions that break down compounds, mostly to allow the cell to generate chemical energy
What are examples of catabolism? (2)
- oxidation of carbohydrates (sugars) during respiration (aerobic or anaerobic)
- fermentation
What happens if glucose is the main nutrient for a bacterium?
It will first be transported across the membrane, and then it will be oxidised to CO2
Which is related to biodegradation, anabolism or catabolism?
Catabolism
What is mineralization?
Conversion of organic compounds to CO2 and water
What are the three main steps of mineralization?
- Glycolysis
- Krebs Cycle or Citric Acid Cycle (ticarboxylic acids cycle; TCA)
- Oxidative phosphorylation (creating the proton motive force)
What is glycolysis?
- Breaking down of glucose into 2 molecules of pyruvate.
- Reactants = glucose
- Products = pyruvate, ATP (energy), NADH, and water
What is the Krebs cycle / tricarboxylic acids cycle
- The complete combustion of pyruvate to CO2 through a cyclic set of reactions (which are the TCA).
- During this cycle, the pyruvate will be decarboxylated, leading to the production of CO2
- Reactant = pyruvate
- Products = ATP, NADH
What is oxidative phosphorylation?
- The reduction of coenzymes (NADH, FADH) that will be further oxidized in the respiratory chain (electron transport system, ETS)
- This produces the proton motive force
What is the electron transport chain / system? (ETC / ETS)
Electrons flow from reduced coenzymes (NAD, FAD) to a terminal electron acceptor such as O2
What does the ETC cause?
The flow of electrons down the chain causes some of the ETC complexes to pump protons (H+) out of the cell resulting in a protein gradient, also known as the Proton Motive Force (PMF)
What is the proton gradient?
A form of electrical energy used by the cell to synthesize ATP.
(it can also allow the cell to do membrane transport, etc)
Why do microbes biodegrade pollutants? (2)
- Because it produces ATP and NADH, so the pollutants are important sources of energy
- They also use the elements that they strip off to build structures
Can bacteria have different types of terminal electron acceptors besides O2?
Yes e.g. nitrate
What is cellular respiration?
Process by which cells release energy by breaking down organic or inorganic molecules
What are the two types of cellular respiration?
Aerobic and anaerobic
What is aerobic respiration?
- Cells break down the glucose molecule and convert it to ATP in presence of O2.
- Is the primary energy-yielding process of all living organisms
What is anaerobic respiration?
- Cells break down the glucose molecule and convert it to ATP in absence of O2.
- Most primitive form of respiration on Earth
What is aerobic respiration in more details and steps? (6 points)
- Uses O2 as terminal electron acceptor
- Reducing power (NADH etc) generated by oxidation of energy source
- Electrons transferred to ETC, then to terminal electron acceptor (TEA) O2 → H2O
- Results in proton (H+)/pH gradient
- H+ gradient fuels processes like ATP synthesis
- The overall process is called oxidative phosphorylation
What is anaerobic respiration in more detail?
- Electrons transferred to compounds other than O2
- Dissimilatory nitrate reduction (denitrification): NO3 -
- Dissimilatory sulfate reduction: SO4 -
- Complex membrane-bound enzymes
- Reduction of the TEA may occur in periplasm rather than cytoplasm, but the effect is the same (electrons transferred, protons pumped, PMF created…)
- Some organic compounds may serve as terminal electron acceptors in anaerobic respiration
*Fumarate → succinate via fumarate reductase
*Membrane-bound enzyme (part of ETC)
*This is not the same as fermentation - Methanogenesis is similar
- Transfer of electrons to CO2 yielding waste CH4
Why are there different electron acceptors besides O2
- Because different TEA are available in different niches
- Their availability can differ with depth
Are the use of different TEA in energy generation key parts of major biogeochemical cycles (C,N,S)?
yes
What is an example of TEA many organisms use
Many organisms utilize metallic terminal electron acceptors (i.e., MnO2, Fe(OH3)), which also vary with depth
Can organisms use more than one compound as TEA?
Some organisms may only be able to utilize one compound, others may be able to utilize more than one, but usually from adjacent zones only
Why are aerobic and anaerobic respiration important to biodegradation? (5 points)
- Most organic pollutants are better degraded aerobically
- Aerobic respiration is generally faster and more efficient and results in more complete oxidation to CO2
- However, anaerobic degradation steps are also very important in the biodegradation of some pollutants
- The ability of bacteria to do this in the absence of O2 makes them extremely useful for biodegradation as many contaminated environments quickly become anaerobic
- Thus, pollutant biodegradation is not limited by O2 as long as there is an alternative terminal electron acceptor and lots of it!
How is the soil a heterogenous microbial habitat? (5 points)
- Contains both aerobic and anaerobic zones, varies greatly, even within a soil aggregate
- Different micro-habitats and food sources
- O2 concentration decreases with depth in a soil
- O2 concentration decreases towards the center of a soil particle due to diffusion, and utilization of O2 on the surface (before it can diffuse in).
- And thus becomes anaerobic!
Environmental heterogeneity (6 points)
- Environmental systems are not homogenous: soil or sediment
- Development of O2 microelectrodes in the 1980’s → became obvious that microgradients were important in nature
- i. e. the use of these microelectrodes in sediment demonstrated that O2 may be completely depleted within 1 mm
- Similar observations were obtained in soil granules, where the centers of such granules are severely depleted in O2
- This rapid decrease of O2 may be explain by a consumption greater than the amount provided through diffusion, since no O2 is produces in sediment or soil below the surface
- Depletion of O2 lead to anaerobic conditions, where a number of other bacterial populations become active
What are some examples of bacteria that use different TEAs? (6)
- denitrifers
- iron-reducing bacteria
- manganese-reducing bacteria
- sulfate-reducing bacteria
- methanogenic archaea
- fermenters
What do denitrifers use as a TEA?
NO3-
When denitrifers reduces NO3-, what products does it make (e.g.) (2)
N2O and N2
What are two examples of names of bacteria that are denitrifiers?
Pseudomonas and Alcaligenes
What do iron-reducing bacteria use as TEA?
Iron lol
What do manganese-reducing bacteria use as TEA?
Manganese lol
What is an example of an iron reducing bacteria (name)?
Geobacter metallireducens GS15
What do sulfate-reducing bacteria use as TEA?
Sulfate! (SO₄²-)
What are some examples of sulfate reducing bacteria? (3)
Desulfovibrio, Desulfuromonas, Desulfosarcina
What do methanogenic archaea use as TEA?
CO2
What do methanogenic archaea use as energy or electron source (2 options)
H2 or ferment acetate
What do fermenters use as TEA? (general)
organic molecules
What are some products of fermentation (5)
Acetate, formate, butyrate, lactate, succinate, caproate, …
What is an example of a fermenting bacteria?
Clostridium
What is so interesting about Shewanella oneidensis?
- It is a supermicrobe that is extremely versatile in regard to electron acceptors (TEA)
- Indeed it can use, O2, NO3-, NO2-, Mn(IV), Mn(III), Fe(III), Fumarate, DMSO, TMAO, S0, S2O3 2-, U(VI), Cr(VI)
What can the geobacter species be used to bioremediate?
Uranium
How does uranium bioremediation work? (2 points)
- Uranium in its highly soluble form is reduced to its highly insoluble form, which will allow it to precipitate out.
- To stimulate geobacters you can add acetate, ethanol, glucose
How to bioremediate arsenic contaminated groundwater by lithotrophic bacteria? (3 points)
- Water cycles through oxygenation tanks back to the source, where aerobic bacteria oxidize Arsenite, iron and Manganese (electron donors)
- Oxidized form of Arsenic (Arsenate), precipitates with iron and manganese for convenient removal
- the TEA is oxygen
Mercury transformations (6 points)
- Mercury has tendency to concentrate in living tissues and it is highly toxic
- Major form of Mercury in the atmosphere is elemental mercury (Hg0), which is volatile and oxidized to mercuric ion (Hg2+) photochemically
- Most mercury enters aquatic environments as Hg2+
- Hg2+ readily absorbs to particulate matter, where it can be metabolized by microorganism
- Under anaerobic conditions, microorganisms form methylmercury (CH3Hg+): an extremely soluble and toxic compound
- Several bacteria can also transform toxic methyl mercury to nontoxic forms, which is being explored to bioremediate mercury contaminated sites
What are the 3 categories used to define microbial nutritional categories?
- source of energy (e.g. light, chemical)
- source of electrons (reducing equivalents) (organic or inorganic)
- source of carbon (itself or other organisms)
Energy sources categories (2)
- Photo-: Light absorption captures energy and excites electron
- Chemo-: Chemical electron donors are oxidized
Electron source (donors) categories (2)
- Litho-: Inorganic molecules donate electrons
- Organo-: Organic molecules donate electrons
Carbon source categories (2)
- Auto-: CO2 is fixed and assembled into organic molecules
- Hetero-: Preformed organic molecules are acquired from outside, broken down for carbon, and the carbon reassembled to make biomass
Chemolithoautotrophs
Bacteria able to oxidize reduced inorganic compounds, such as NH4 +, H2S or H2 to synthesize ATP for biosynthesis
Examples of chemolithoautotrophs
- Ammonium-oxidizing nitrifying bacteria
- Nitrite-oxidizing nitrifying bacteria
Examples of Ammonium-oxidizing nitrifying bacteria
Nitrosomonas sp., Nitrovibrio sp.
Ammonium-oxidizing nitrifying bacteria: energy source and what they do with it
Use NH4 + as sole energy source and oxidize it to NO2 -
Why are Ammonium-oxidizing nitrifying bacteria interesting in terms of bioremediation?
Because they have a monooxygenase (ammonia monooxygenase, AMO), which may attack some pollutants such as trichloroethylene (TCE)
What is an example of Nitrite-oxidizing nitrifying bacteria
Nitrobacter sp.
What energy source do Nitrite-oxidizing nitrifying bacteria use and what do they do with it?
They use NO2 - as sole energy source and oxidize it to NO3
How do ammonium-oxidizing nitrifying bacteria and nitrite-oxidizing nitrifying bacteria play a critical role in the nitrogen cycle?
by converting NH4 + to NO3 - which is often the rate-limiting step in nitrogen cycle
Electron acceptors in marine sediment: their order in terms of depth (from surface to deepest) (4)
- O2
- NO3 -
- SO4 2-
- CO2
Common sources of ground water contamination (5)
- fertilizers
- pesticides
- road salt
- surface water runoff
- excavations, mining
Summary Microbial physiology basics: Electron donors (what do they do)
- Reduces organic compounds: carbohydrates, CH4
- Reduced inorganic compounds: H 2S
Summary Microbial physiology basics:
Electron acceptors what are they for aerobic and anaerobic respiration?
Terminal electron acceptor during respiration
* Aerobic respiration: O 2 (to H 2O)
* Anaerobic respiration: NO 3- (to NH 4+)
How would you stimulate oil biodegradation in a contaminated aquifer?
- In terms of remediation, it is important to know what is in the aquifer! (e.g. oxygen…
- What can you do bc rn there is missing TEA
- The aerobic lack oxygen
- 2 choices:
- Start pumping oxygen into the system to stimulate aerobic organisms
- If Other organisms, pump what is limiting their biodegrative activity
Sequential reduction of terminal electron acceptors in contaminated sediments and aquifers (4 points)
- A profile of sediment show that after the depletion of O2 , NO 3- is depleted, and then depletion of SO 4- results in sulfide accumulation
- Finally, utilization of CO2 results in CH 4 accumulation, as all the other potential electron acceptors have been depleted
- After the flooding of a soil, a similar succession of reductions occurs, often leading to the production of methane
- The sequential reduction of different electron acceptors indicates a succession of heterotrophic bacterial populations:
- Denitrifiers
- Iron reducers
- Sulfate reducers
- Methanogens
Summary – Microbial bioenergetics / thermodynamics (5 points)
- Needed to energize cytoplasmic membrane via proton gradient
- Proton gradient interconverted with ATP, NAD(P)H pools
- NAD(P)H = reducing power required for some biochemical reactions
- Microbes use energy ATP, NAD(P)H for cellular functions such as biosynthesis: nucleic acids, proteins, lipids …
- Also used for CO 2-fixation and initiation of some catabolic pathways, depending upon the species
Summary Microbial physiology basics:
- Organic compound during fermentation
- Temperature, pressure, pH, salt
- Surfaces to colonize (biofilms)
